Bottom Line:
We have observed that the LUD domain has an increased abundance in the human gut microbiome.We propose a model for the substrate and cofactor binding and regulation in LUD domain.The significance of LUD-containing proteins in the human gut microbiome, and the implication of lactate metabolism in the radiation-resistance of Deinococcus radiodurans are discussed.

Background: A novel highly conserved protein domain, DUF162 [Pfam: PF02589], can be mapped to two proteins: LutB and LutC. Both proteins are encoded by a highly conserved LutABC operon, which has been implicated in lactate utilization in bacteria. Based on our analysis of its sequence, structure, and recent experimental evidence reported by other groups, we hereby redefine DUF162 as the LUD domain family.

Results: JCSG solved the first crystal structure [PDB:2G40] from the LUD domain family: LutC protein, encoded by ORF DR_1909, of Deinococcus radiodurans. LutC shares features with domains in the functionally diverse ISOCOT superfamily. We have observed that the LUD domain has an increased abundance in the human gut microbiome.

Conclusions: We propose a model for the substrate and cofactor binding and regulation in LUD domain. The significance of LUD-containing proteins in the human gut microbiome, and the implication of lactate metabolism in the radiation-resistance of Deinococcus radiodurans are discussed.

Figure 8: Docking of NADH to the hypothetical active site near the dimer interface. The monomers are colored in cyan and brown, respectively. Highly conserved residues, Y55, H201, R204 nearby are highlighted in green and labeled.

Mentions:
Inspection of the LutC protein dimer structure identified a highly conserved cavity (lined by residues Y55, H201, and R204) near the dimer interface. We proposed this cavity to be the putative active site (Figure 7), where the oxidative conversion of lactate into pyruvate occurs [9], based on the following observations: First, the residues surrounding this cavity are highly conserved, suggesting they are functionally important. Second, this cavity is large enough to accommodate both NAD + and lactate, hypothetical cofactor and substrate (Figure 8). NAD is among the top 5 possible ligands for LutC dimer as predicted by IsoCleft [24]. Top ligand predicted by Isocleft predicted was NDP (NADPH). Third, in the docking model the highly conserved H201 in LutC protein is located close to the substrate-cofactor reaction site and could hence serve as the catalytic histidine. Fourth, the 11-residue disordered loop (between S187 and G199) near this cavity could function as a substrate binding regulator, analogous to the role played by the disordered loop in the active site of lactate dehydrogenase (LDH), which converts pyruvate to lactate [25]. Taken together, it is likely that this pocket is indeed the active site.

Figure 8: Docking of NADH to the hypothetical active site near the dimer interface. The monomers are colored in cyan and brown, respectively. Highly conserved residues, Y55, H201, R204 nearby are highlighted in green and labeled.

Mentions:
Inspection of the LutC protein dimer structure identified a highly conserved cavity (lined by residues Y55, H201, and R204) near the dimer interface. We proposed this cavity to be the putative active site (Figure 7), where the oxidative conversion of lactate into pyruvate occurs [9], based on the following observations: First, the residues surrounding this cavity are highly conserved, suggesting they are functionally important. Second, this cavity is large enough to accommodate both NAD + and lactate, hypothetical cofactor and substrate (Figure 8). NAD is among the top 5 possible ligands for LutC dimer as predicted by IsoCleft [24]. Top ligand predicted by Isocleft predicted was NDP (NADPH). Third, in the docking model the highly conserved H201 in LutC protein is located close to the substrate-cofactor reaction site and could hence serve as the catalytic histidine. Fourth, the 11-residue disordered loop (between S187 and G199) near this cavity could function as a substrate binding regulator, analogous to the role played by the disordered loop in the active site of lactate dehydrogenase (LDH), which converts pyruvate to lactate [25]. Taken together, it is likely that this pocket is indeed the active site.

Bottom Line:
We have observed that the LUD domain has an increased abundance in the human gut microbiome.We propose a model for the substrate and cofactor binding and regulation in LUD domain.The significance of LUD-containing proteins in the human gut microbiome, and the implication of lactate metabolism in the radiation-resistance of Deinococcus radiodurans are discussed.

Background: A novel highly conserved protein domain, DUF162 [Pfam: PF02589], can be mapped to two proteins: LutB and LutC. Both proteins are encoded by a highly conserved LutABC operon, which has been implicated in lactate utilization in bacteria. Based on our analysis of its sequence, structure, and recent experimental evidence reported by other groups, we hereby redefine DUF162 as the LUD domain family.

Results: JCSG solved the first crystal structure [PDB:2G40] from the LUD domain family: LutC protein, encoded by ORF DR_1909, of Deinococcus radiodurans. LutC shares features with domains in the functionally diverse ISOCOT superfamily. We have observed that the LUD domain has an increased abundance in the human gut microbiome.

Conclusions: We propose a model for the substrate and cofactor binding and regulation in LUD domain. The significance of LUD-containing proteins in the human gut microbiome, and the implication of lactate metabolism in the radiation-resistance of Deinococcus radiodurans are discussed.